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The Glycopeptide Spectrum Annotation program (gpAnnotate) is designed to annotate individual glycoproteomics MS/MS spectrum for several established mass spectrometry fragmentation modes:
CID: collision induced dissociation
HCD: beam-type CID or higher-energy collision dissociation
ETD: electron transfer dissociation
ETciD: electron-transfer-CID, and
EThcD: electron-transfer-HCD.
In addition to preset options that are fixed for the above modes, gpAnnotate also allows ‘Custom’ definition of fragmentation rules in order to accommodate additional user preferences. Thus, in principle, it can handle a wide variety of scenarios.
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